Protein function from the perspective of molecular interactions and genetic networks.

Protein function is a complex notion, which is now receiving renewed attention from a bioinformatics and genomics perspective. After a general discussion of the principles of experimental methods employed to decipher gene/protein function, the contributions made by new, high-throughput methods in terms of function discovery are discussed. Recent work on functional ontologies and the necessity to describe function within the context of hierarchical levels of complexity are presented. The concepts of molecular interactions and genetic networks are then discussed, leading to a useful new framework with which to describe protein function using new tools such as 2D interaction maps. Finally, it is proposed that interaction data could be used to develop new methods for the functional classification of proteins. An example of functional comparisons on a real data set of yeast chromosomal proteins is presented.

Grasping at molecular interactions and genetic networks in Drosophila melanogaster using FlyNets, an Internet database.

FlyNets (http://gifts.univ-mrs.fr/FlyNets/FlyNets_home_page.++ +html) is a WWW database describing molecular interactions (protein-DNA, protein-RNA and protein-protein) in the fly Drosophila melanogaster. It is composed of two parts, as follows. (i) FlyNets-base is a specialized database which focuses on molecular interactions involved in Drosophila development. The information content of FlyNets-base is distributed among several specific lines arranged according to a GenBank-like format and grouped into five thematic zones to improve human readability. The FlyNets database achieves a high level of integration with other databases such as FlyBase, EMBL, GenBank and SWISS-PROT through numerous hyperlinks. (ii) FlyNets-list is a very simple and more general databank, the long-term goal of which is to report on any published molecular interaction occuring in the fly, giving direct web access to corresponding s in Medline and in FlyBase. In the context of genome projects, databases describing molecular interactions and genetic networks will provide a link at the functional level between the genome, the proteome and the transcriptome worlds of different organisms. Interaction databases therefore aim at describing the contents, structure, function and behaviour of what we herein define as the interactome world.

Mutations in ccf, a novel Drosophila gene encoding a chromosomal factor, affect progression through mitosis and interact with Pc-G mutations.

We report herein the isolation of ccf, a new gene located in region 82E and essential for Drosophila development. This gene, expressed throughout development, encodes a novel product of 68 kDa which is found in the nucleus during interphase and labels, in a novel pattern, centrosomes and chromosome arms during mitosis. Mutations in ccf give rise to late larvae with small imaginal discs and to adults showing appendages of reduced size, consistent with CCF involvement in cell proliferation. Neuroblast squash analyses show that CCF is required for proper condensation of mitotic chromosomes and, therefore, for progression through mitosis. Furthermore, we observe that adult ccf mutants as well as animals overexpressing CCF during larval stages exhibit homeotic transformations. We also find that mutations in the Pc-G genes Polycomb, polyhomeotic and Enhancer of zeste are enhanced by ccf mutations. Finally, we show that the CCF protein binds to specific sites on polytene chromosomes, many of which are shared with the Posterior sex combs Pc-G protein. Together, these results suggest a role for the CCF protein in the maintenance of chromosome structure during mitosis and interphase.

FlyNets and GIF-DB, two internet databases for molecular interactions in Drosophila melanogaster.

GIF-DB and FlyNets are two WWW databases describing molecular (protein-DNA, protein-RNA and protein-protein) interactions occuring in the fly Drosophila melanogaster (http://gifts.univ-mrs.fr/GIFTS_home_page.html ). GIF-DB is a specialised database which focuses on molecular interactions involved in the process of embryonic pattern formation, whereas FlyNets is a new and more general database, the long-term goal of which is to report on any published molecular interaction occuring in the fly. The information content of both databases is distributed in specific lines arranged into an EMBL- (or GenBank-) like format. These databases achieve a high level of integration with other databases such as FlyBase, EMBL, GenBank and SWISS-PROT through numerous hyperlinks. In addition, we also describe SOS-DGDB, a new collection of annotated Drosophila gene sequences, in which binding sites for regulatory proteins are directly visible on the DNA primary sequence and hyperlinked both to GIF-DB and TRANSFAC database entries.

Detecting Gene Symbols and Names in Biological Texts: A First Step toward Pertinent Information Extraction.

Gathering data on molecular interactions to be fed into a specialized database has motivated the development of a computer system to help extracting pertinent information from texts, relying on advanced linguistic tools, completed with object-oriented knowledge modeling capabilities. As a first step toward this challenging objective, a program for the identification of gene symbols and names inside sentences has been devised. The main difficulty is that these names and symbols do not appear to follow construction rules. The program is thus made up of a series of sieves of different natures, lexical, morphological and semantic, to distinguish among the words of a sentence those which can only be potential gene symbols or names. Its performance has been evaluated, in terms of coverage and precision ratios, on a corpus of texts concerning D. melanogaster for which the list of names of known genes is available for checking.

GIF-DB, a WWW database on gene interactions involved in Drosophila melanogaster development.

GIF-DB (Gene Interactions in the Fly Database) is a new WWW database (http://www-biol.univ-mrs.fr/ approximately lgpd/GIFTS_home_page. html ) describing gene molecular interactions involved in the process of embryonic pattern formation in the flyDrosophila melanogaster. The detailed information is distributed in specific lines arranged into an EMBL- (or SWISS-PROT-) like format. GIF-DB achieves a high level of integration with other databases such as FlyBase, EMBL and SWISS-PROT through numerous hyperlinks. The original concept of interaction databases examplified by GIF-DB could be extended to other biological subjects and organisms so as to study gene regulatory networks in an evolutionary perspective.

A knowledge base for D. melanogaster gene interactions involved in pattern formation.

The understanding of pattern formation in Drosophila requires the handling of the many genetic and molecular interactions which occur between developmental genes. For that purpose, a knowledge base (KNIFE) has been developed in order to structure and manipulate the interaction data. KNIFE contains data about interactions published in the literature and gathered from various databases. These data are structured in an object knowledge representation system into various interrelated entities. KNIFE can be browsed through a WWW interface in order to select, classify and examine the objects and their references in other bases. It also provides specialised biological tools such as interaction network manipulation and diagnosis of missing interactions.

The Drosophila teashirt homeotic protein is a DNA-binding protein and modulo, a HOM-C regulated modifier of variegation, is a likely candidate for being a direct target gene.

The Drosophila teashirt (tsh) gene has an homeotic function which, in combination with HOM-C genes, determines thoracic and abdominal (trunk) identities. Analysis of TSH protein distribution during embryogenesis using a specific polyclonal antibody shows that it is nuclear. The protein is present with regional modulation in several tissues within the trunk, suggesting additional tsh functions to those already studied. We identified a candidate tsh target shared with some HOM-C genes, the modifier of variegation gene modulo (mod). The TSH zinc-finger protein recognizes in vitro two specific sites within a 5' control element of the mod gene which responds in vivo to tsh activity. TSH is therefore a DNA binding protein and might directly control mod expression.

Homeotic complex and teashirt genes co-operate to establish trunk segmental identities in Drosophila.

Homeotic genes determine the identities of metameres in Drosophila. We have examined functional aspects of the homeotic gene teashirt by ectopically expressing its product under the control of a heat-shock promoter during embryogenesis. Our results confirm that the gene is critical for segmental identity of the larva. Under mild heat-shock conditions, the Teashirt protein induces an almost complete transformation of the labial to prothoracic segmental identity, when expressed before 8 hours of development. Positive autoregulation of the endogenous teashirt gene and the presence of Sex combs reduced protein in the labium explain this homeosis. Patterns in the maxillary and a more anterior head segment are partly replaced with trunk ones. Additional Teashirt protein has no effect on the identity of the trunk segments where the gene is normally expressed; teashirt function is overridden by some homeotic complex acting in the posterior trunk. Strong heat-shock regimes provoke novel defects: ectopic sense organs differentiate in posterior abdominal segments and trunk pattern elements differentiate in the ninth abdominal segment. Teashirt acts in a partially redundant way with certain homeotic complex proteins but co-operates with them for the establishment of specific segment types. We suggest that Teashirt and HOM-C proteins regulate common sets of downstream target genes.

Factors influencing T-DNA transfer in Agrobacterium-mediated transformation of sugarbeet.

Agrobacterium-mediated transformation of sugarbeet (Beta vulgaris L.) was investigated for T-DNA transfer efficiency, using an intron containing ß-glucuronidase gene. Preculture and coculture of hypocotyl and cotyledon explants with acetosyringone upon infection was studied. Seven seed lots which included several hundred genotypes, were screened, and were all susceptible to T-DNA transfer but with variable frequencies. Cotyledon explants were more readily transformed than those from hypocotyls. Transformation frequency of hypocotyl explants increased with acetosyringone. Both preculture treatment and acetosyringone improved transformation in cotyledon explants. Callus assayed with fluorometric procedures confirmed that the GUS gene had been transferred into sugarbeet.

Plant regeneration from sugarbeet (Beta vulgaris L.) hypocotyls cultured in vitro and flow cytometric nuclear DNA analysis of regenerants.

A simple and reproducible protocol for regeneration of sugarbeet plants from hypocotyl expiants derived from 21 day-old-seedlings has been developed. Expiants were cultured on MS medium containing 0.3 mg/l N6-Benzylaminopurine, 0.1 mg/l Naphthalene Acetic Acid, 50 mg/l adenine and 0.5% (w/v) fructose, 0.5% (w/v) sucrose and 0.5% (w/v) glucose to induce the formation of organogenic calli (2.3% to 46.5% organogenic efficiency, depending on populations). Shoot formation was induced in callus cultures of more than 1600 genotypes. Physiological age affected culture response and different genotypes had different temperature optima for organogenesis. Following transfer of regenerated plants to the greenhouse, DNA determinations were made to study the stability of ploidy. Differences in ploidy were observed in plants derived from both shortterm and long-term callus cultures; diploid true-to-type regenerants were 96% and 83%, respectively, from shortterm and long-term callus cultures.

The gene teashirt is required for the development of Drosophila embryonic trunk segments and encodes a protein with widely spaced zinc finger motifs.

We have discovered a reporter gene insertion that is expressed in the trunk region of Drosophila embryos. Genetic and molecular details of a new regulatory gene neighboring the reporter gene insertion, which we call teashirt (tsh), are described. In situ hybridization of a tsh probe to embryos shows that this gene is expressed in a way similar to the reporter gene. Mutations of tsh show that the gene is required for normal development of the ventral trunk region of embryos, which correlates with the spatial expression of the gene in the anteroposterior axis but not in the dorsoventral axis. Sequencing of a tsh cDNA shows that the putative protein possesses three distantly spaced CX2CX12HX5H zinc finger motifs.

Sequence and secondary structure of the central domain of Drosophila 26S rRNA: a universal model for the central domain of the large rRNA containing the region in which the central break may happen.

An 890-bp sequence from the central region of Drosophila melanogaster 26S ribosomal DNA (rDNA) has been determined and used in an extensive comparative analysis of the central domain of the large subunit ribosomal RNA (lrRNA) from prokaryotes, organelles, and eukaryotes. An alignment of these different sequences has allowed us to precisely map the regions of the central domain that have highly diverged during evolution. Using this sequence comparison, we have derived a secondary structure model of the central domain of Drosophila 26S ribosomal RNA (rRNA). We show that a large part of this model can be applied to the central domain of lrRNA from prokaryotes, eukaryotes, and organelles, therefore defining a universal common structural core. Likewise, a comparative study of the secondary structure of the divergent regions has been performed in several organisms. The results show that, despite a nearly complete divergence in their length and sequence, a common structural core is also present in divergent regions. In some organisms, one or two of the divergent regions of the central domain are removed by processing events. The sequence and structure of these regions (fragmentation spacers) have been compared to those of the corresponding divergent regions that remain part of the mature rRNA in other species.

Hox-7, a mouse homeobox gene with a novel pattern of expression during embryogenesis.

A new mouse Hox locus, Hox-7, is defined on chromosome 5 by a gene homologous to the Drosophila gene msh, which contains a homeobox sequence distantly related to that of Antennapedia. By in situ hybridization, expression of Hox-7 is detected in the neural fold of embryos, and also in cephalic neural crest. In addition, expression takes place in the developing valves of the embryonic heart. Mandibular and hyoid arches are strongly labelled, expression becoming restricted to the most distal part of mouth and face processes as development proceeds. Intense labelling is also observed in developing limb buds, in the distal region which has been shown to be essential for limb morphogenesis. The pronounced accumulation and regional localization of Hox-7 transcripts in mandibular and limb processes point to a specific morphogenetic role for this mouse homeobox gene.

Sequence studies on the soybean chloroplast 16S-23S rDNA spacer region : Comparison with other angiosperm sequences and proposal of a generalized RNA secondary structure model for the intergenic regions.

The sequence of the ribosomal spacer region of soybean chloroplast DNA including the 3' end of the 16S rRNA gene, the tRNA(Ala) and tRNA(Ile) genes (but not their introns), the three intergenic regions and the 5' end of the 23S rRNA gene, has been determined. This sequence has been compared to corresponding regions of other angiosperm chloroplast DNAs. Secondary structure models are proposed for the entirety of the intergenic regions a, b and c and for the flanking rRNA regions. A model for a common secondary structure of the ribosomal spacer intergenic regions from chloroplasts of higher plants is proposed, which is supported by comparative evidence.

A remarkable amino acid sequence homology between a phage T4 tail fibre protein and ORF314 of phage lambda located in the tail operon.

We have found that the amino acid (aa) sequence of the tip of phage T4 tail fibre (gene 37) shows more than 50% homology with the aa sequence predicted from an open reading frame (ORF314) in the phage lambda genome. ORF314 is near the 3' end of the late morphogenetic operon, beyond gene J coding for the lambda tail fibre. The homologous sequences are for the most part composed of repeated aa, the most remarkable of which is a Gly-X-His-Y-His motif where X and Y are small, uncharged aa, found six times in the T4 protein and seven times in the lambda ORF314 sequence.

Apple II PASCAL programs for molecular biologists.

A collection of PASCAL programs designed for the Apple II microcomputer is presented. These DNA sequence handling and analysis programs are interactive and may be used even by people with no computer experience. The package allows the user to enter a sequence from the keyboard, to modify it, to generate the reverse complement, to create new sequences from parts of other ones, to display or print sequences in various formats. Some analysis tasks are also performed: Translation, searches for restriction sites, for homology with subsequences, either perfect or with an adjustable match percentage. In addition, two programs are also included: The first one allows DNA data sequences generated with a BASIC program under the CP/M operating system to be used with these PASCAL programs. The second one is designed for the automatic assembly of DNA fragments sequences, obtained with the GILBERT-MAXAM or M13 techniques, into a complete sequence.

[Sequence of the central break region of the precursor of Drosophila 26S ribosomal RNA]. / Séquence de la région de la coupure centrale du précurseur de l'ARN ribosomique 26S de Drosophile.

A 431 nucleotide sequence from the central break region of Drosophila 26S rRNA precursor has been established by sequencing the corresponding region of the 26S gene. The analysis of rDNA-mature 26S rRNA hybrids submitted to S1 nuclease digestion has allowed us to show that a 75 +/- 3 nucleotide A-U rich RNA fragment is excised during the processing of the precursor.

Sequence homologies between eukaryotic 5.8S rRNA and the 5' end of prokaryotic 23S rRNa: evidences for a common evolutionary origin.

The question of the evolutionary origin of eukaryotic 5.8S rRNA was re-examined after the recent publication of the E. coli 23S rRNA sequence (26,40). A region of the 23S RNA located at its 5' end was found to be approximately 50% homologous to four different eukaryotic 5.8S rRNAs. A computer comparison analysis indicates that no other region of the E. coli ribosomal transcription unit (greater than 5 000 nucleotides in length) shares a comparable homology with 5.8S rRNA. Homology between the 5' end of e. coli 23S and four different eukaryotic 5.8S rRNAs falls within the same range as that between E. coli 5S RNA from the same four eukaryotic species. All these data strongly suggest that the 5' end of prokaryotic 23S rRNA and eukaryotic 5.8S RNA have a common evolutionary origin. Secondary structure models are proposed for the 5' region of E. coli 23S RNA.